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Huang X, Braga LPP, Ding C, Yang B, Ge T, Di H, He Y, Xu J, Philippot L, Li Y. Impact of Viruses on Prokaryotic Communities and Greenhouse Gas Emissions in Agricultural Soils. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407223. [PMID: 39373699 DOI: 10.1002/advs.202407223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 09/09/2024] [Indexed: 10/08/2024]
Abstract
Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulating greenhouse gas emissions and prokaryotic communities. The results showed that the addition of viruses has a strong impact on methane (CH4) and nitrous oxide (N2O) emissions and, to a minor extent, carbon dioxide (CO2) emissions, along with dissolved carbon and nitrogen pools, depending on soil fertilization history. The addition of a high viral load resulted in a decrease in microbial biomass carbon (MBC) by 31.4%, with changes in the relative abundance of 16.6% of dominant amplicon sequence variants (ASVs) in comparison to control treatments. More specifically, large effects of viral pressure are observed on some specific microbial communities with decreased relative abundance of prokaryotes that dissimilate sulfur compounds and increased relative abundance of Nanoarchaea. Structural equation modeling further highlighted the differential direct and indirect effects of viruses on CO2, N2O, and CH4 emissions. These findings underpin the understanding of the complex microbe-virus interactions and advance current knowledge on soil virus ecology.
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Affiliation(s)
- Xing Huang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lucas P P Braga
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Chenxiao Ding
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bokai Yang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Laurent Philippot
- Université Bourgogne, INRAE, Institut Agro Dijon, Agroécologie, Dijon, 21000, France
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
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Karmakar S, Mukherjee P, Mishra V, Gupta RK, Kumar R, Srivastava P, Sharma RS. Microhabitat influences on phage-bacteria dynamics in an abandoned mine for ecorestoration. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122659. [PMID: 39340888 DOI: 10.1016/j.jenvman.2024.122659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 09/22/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024]
Abstract
Understanding the complex interactions between bacteriophages (phages) and bacteria within varied environmental niches is critical yet underexplored for improving microbe-assisted ecological restoration. This study investigates the influence of microhabitat heterogeneity within an abandoned mine on phage-bacteria interaction patterns, focusing on Pseudomonas-enriched bacterial communities. By isolating viral communities and purifying bacteria from soils of three distinct microhabitats, we assessed the regulatory role of environmental factors on these interactions, crucial for bacterial success in environmental applications. We characterized microhabitat variability by analyzing soil particle size fractions, minerals composition, and elemental content using X-ray diffraction and energy-dispersive X-ray analyses. 16S rRNA sequencing and cross-infection assays revealed that although bacterial communities across different microhabitats are taxonomically similar, their interaction patterns with phages are distinct. Phage communities showed nonselective infectivity across soil types, while bacterial communities exhibited selective adaptation, facilitating colonization across diverse microhabitats. Minerals such as mica, kaolinite, and hematite were found to increase phage infectivity, whereas mixed-layer clay correlated with early lysis. Additionally, higher levels of iron (Fe) and potassium (K) were linked to bacterial resistance strategies. Our findings highlight the importance of understanding asymmetric adaptive strategies between bacteria and phages, driven by microhabitat heterogeneity, for enhancing microbial-mediated nature-based restoration of degraded ecosystems.
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Affiliation(s)
- Swagata Karmakar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007, India; Department of Environmental Studies, Ram Lal Anand College, University of Delhi, 110021, India
| | - Paromita Mukherjee
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007, India; Department of Environmental Science, Ramjas College, University of Delhi, Delhi, 110007, India
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007, India; Centre for Inter-Disciplinary Studies of Mountain & Hill Environment (CISMHE), University of Delhi, Delhi, India; DDA Biodiversity Parks Programme, CEMDE, University of Delhi, Delhi, 110007, India.
| | - Rakesh Kumar Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, 110021, India
| | - Rohit Kumar
- Department of Geology, University of Delhi, Delhi, 110007, India
| | | | - Radhey Shyam Sharma
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi, 110007, India.
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Valencia-Toxqui G, Ramsey J. How to introduce a new bacteriophage on the block: a short guide to phage classification. J Virol 2024:e0182123. [PMID: 39264154 DOI: 10.1128/jvi.01821-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024] Open
Abstract
Bacteriophage (phage) studies established the field of molecular biology and continue to propel life science research forward due to their diversity, abundance, and potential applications. In this Gem article, we orient newcomers to four common ways phages are currently classified: infection cycle, morphology, taxonomy, and supergroup. By using these classifications, researchers can determine where any novel phage fits into the scheme of the known "phage-verse".
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Affiliation(s)
- Guadalupe Valencia-Toxqui
- Department of Biology, Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Jolene Ramsey
- Department of Biology, Center for Phage Technology, Texas A&M University, College Station, Texas, USA
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Haq IU, Rahim K, Paker NP. Exploring the historical roots, advantages and efficacy of phage therapy in plant diseases management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112164. [PMID: 38908799 DOI: 10.1016/j.plantsci.2024.112164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
In the drug-resistance era, phage therapy has received considerable attention from worldwide researchers. Phage therapy has been given much attention in public health but is rarely applied to control plant diseases. Herein, we discuss phage therapy as a biocontrol approach against several plant diseases. The emergence of antibiotic resistance in agriculturally important pathogenic bacteria and the toxic nature of different synthetic compounds used to control microbes has driven researchers to rethink the century-old strategy of phage therapy''. Compared to other treatment strategies, phage therapy offers remarkable advantages such as high specificity, less chances of drug resistance, non-harmful nature, and benefit to soil microbial flora. The optimizations and protective formulations of phages are significant accomplishments; however, steps towards a better understanding of the physiologic characteristics of phages need to be preceded to commercialize their use. The future of phage therapy in the context of plant disease management is promising and could play a significant role in sustainable agriculture. Ongoing research will likely affirm the safety of phage therapy, ensuring that it does not harm non-target organisms, including beneficial soil microbes. Phage therapy could become vital in addressing global food security challenges, particularly in regions heavily impacted by plant bacterial diseases. Efforts to create formulations that enhance the stability and shelf-life of phages will be crucial, especially for their use in varied environmental conditions.
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Affiliation(s)
- Ihtisham Ul Haq
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, Gliwice 44-100, Poland; Joint Doctoral School, Silesian University of Technology, Akademicka 2A, Gliwice 44-100, Poland; Programa de Pos-graduacao em Invacao Tecnologia, Universidade de Minas Gerais, Belo Horizonte, Brazil.
| | - Kashif Rahim
- School of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Najeeba Parre Paker
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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Bucher MJ, Czyż DM. Phage against the Machine: The SIE-ence of Superinfection Exclusion. Viruses 2024; 16:1348. [PMID: 39339825 PMCID: PMC11436027 DOI: 10.3390/v16091348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/10/2024] [Accepted: 08/20/2024] [Indexed: 09/30/2024] Open
Abstract
Prophages can alter their bacterial hosts to prevent other phages from infecting the same cell, a mechanism known as superinfection exclusion (SIE). Such alterations are facilitated by phage interactions with critical bacterial components involved in motility, adhesion, biofilm production, conjugation, antimicrobial resistance, and immune evasion. Therefore, the impact of SIE extends beyond the immediate defense against superinfection, influencing the overall fitness and virulence of the bacteria. Evaluating the interactions between phages and their bacterial targets is critical for leading phage therapy candidates like Pseudomonas aeruginosa, a Gram-negative bacterium responsible for persistent and antibiotic-resistant opportunistic infections. However, comprehensive literature on the mechanisms underlying SIE remains scarce. Here, we provide a compilation of well-characterized and potential mechanisms employed by Pseudomonas phages to establish SIE. We hypothesize that the fitness costs imposed by SIE affect bacterial virulence, highlighting the potential role of this mechanism in the management of bacterial infections.
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Affiliation(s)
- Michael J Bucher
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Daniel M Czyż
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Ikpe F, Williams T, Orok E, Ikpe A. Antimicrobial resistance: use of phage therapy in the management of resistant infections. Mol Biol Rep 2024; 51:925. [PMID: 39167154 DOI: 10.1007/s11033-024-09870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
The emergence and increase in antimicrobial resistance (AMR) is now widely recognized as a major public health challenge. Traditional antimicrobial drugs are becoming increasingly ineffective, while the development of new antibiotics is waning. As a result, alternative treatments for infections are garnering increased interest. Among these alternatives, bacteriophages, also known as phages, are gaining renewed attention and are reported to offer a promising solution to alleviate the burden of bacterial infections. This review discusses the current successes of phage therapy (PT) against multidrug-resistant organisms (MDROs), such as Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp. The review also compares the efficacy of PT with that of chemical antibiotics, reporting on its benefits and limitations, while highlighting its impact on the human gut microbiome and immune system. Despite its potential, phage therapy is reported to face challenges such as the narrow antibacterial range, the complexity of developing phage cocktails, and the need for precise dosing and duration protocols. Nevertheless, continued research, improved regulatory frameworks, and increased public awareness are essential to realize its full potential and integration into standard medical practice, paving the way for innovative treatments that can effectively manage infections in an era of rising antimicrobial resistance.
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Affiliation(s)
- Favour Ikpe
- Department of Pharmaceutical Microbiology and Biotechnology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Tonfamoworio Williams
- Department of Pharmaceutical Microbiology and Biotechnology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Edidiong Orok
- Department of Clinical Pharmacy and Public Health, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria.
| | - Augustine Ikpe
- Department of Sciences, Champion Group of Schools, Okene, Kogi State, Nigeria
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Wang Y, Tong G, Jiang X, Tu C, Cai H, Fang W, Tan H, Weng Q, Wei X, Lin M. Biologic and genomic characterization of a novel virulent Aeromonas hydrophila phage phiA051, with high homology to prophages. Front Vet Sci 2024; 11:1415685. [PMID: 39091387 PMCID: PMC11292799 DOI: 10.3389/fvets.2024.1415685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Aeromonas hydrophila is particularly harmful to freshwater aquaculture, and the search for phage is an effective biological control method, but reports of possible temperate phages and their mutants are rare in this field. In this study, a virulent phage highly homologous to prophage in the genomes of A. hydrophila was collected and preliminary biological characterization was carried out to understand its nature. Materials and methods Water samples taken from eel ponds in Fujian, China were combined with the strain. Spot test method and double-layer agar plate assay was used for confirmation and purification. Phage virions were observed using transmission electron microscope. A total of 68 strains of Aeromonas spp. were used to determine the host range. MOI groups of 1,000, 100, 10, 1, 0.1, 0.01, 0.001, 0.0001, 0.00001 were prepared to detect the optimal MOI. The conditions of thermal stability assay were set as 30, 40, 50, 60, 70 and 80°C for 1 h, respectively, and conditions of acid and alkali stability assay were set as 2.0, 4.0, 6.0, 8.0, 10.0 and 12.0 of pH. MOI of 0.01 and 0.1, respectively, are set to determine the inhibitory capacity of phage. Results A novel virulent A. hydrophila phage designated phiA051 has been isolated from aquaculture water. Electron microscopic observation showed that the phage phiA051 was composed of an icosahedral capsid. The phage phiA051 possesses an optimal multiplicity of infection (MOI) of 0.01, and its burst size was 108 PFU/cell. The phage maintained a high viability at temperatures of 30-50°C or pH 6.0-10.0 for 1 h. Phage phiA051 has certain potentials in rapidly inhibiting the spread of pathogen early in the outbreak, and it has a linear dsDNA with GC content of 60.55% and a total length of 32,212 bp, including 46 ORFs. Discussion The phage phiA051 behaved as a virulent phage. However, the BLASTN result showed that 23 of the top 25 hits were genomes of Aeromonas strains. It was suggested that phiA051 was probably derived from some prophage in the chromosome of Aeromonas. Further investigation of the mechanism how phage phiA051 transforms from a temperate phage to a virulent phage will provide a unique perspective and idea to explore the potential of prophages.
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Affiliation(s)
- Yuzhi Wang
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Guixiang Tong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xinglong Jiang
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, China
| | - Chuandeng Tu
- Xiamen Key Laboratory of Intelligent Fishery, Xiamen Ocean Vocational College, Xiamen, China
| | - Hongjiao Cai
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Wenhong Fang
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai, China
| | - Honglian Tan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qibiao Weng
- Key Laboratory of Eel Aquaculture and Processing of Fujian Province, Fuzhou, China
| | - Xinxian Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Mao Lin
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, China
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso J. Biochemical characterisation and production kinetics of high molecular-weight (HMW) putative antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates. BMC Microbiol 2024; 24:259. [PMID: 38997685 PMCID: PMC11245835 DOI: 10.1186/s12866-024-03340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/16/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Bacterial genomes often encode structures similar to phage capsids (encapsulins) and phage tails which can be induced spontaneously or using genotoxic compounds such as mitomycin C. These high molecular-weight (HMW) putative antibacterial proteins (ABPs) are used against the competitive strains under natural environment. Previously, it was unknown whether these HMW putative ABPs originating from the insect pathogenic Gram-positive, spore-forming bacterium Brevibacillus laterosporus (Bl) isolates (1821L, 1951) are spontaneously induced during the growth and pose a detrimental effect on their own survival. Furthermore, no prior work has been undertaken to determine their biochemical characteristics. RESULTS Using a soft agar overlay method with polyethylene glycol precipitation, a narrow spectrum of bioactivity was found from the precipitated lysate of Bl 1951. Electron micrographs of mitomycin C- induced filtrates showed structures similar to phage capsids and contractile tails. Bioactivity assays of cell free supernatants (CFS) extracted during the growth of Bl 1821L and Bl 1951 suggested spontaneous induction of these HMW putative ABPs with an autocidal activity. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of spontaneously induced putative ABPs showed appearance of ~ 30 kDa and ~ 48 kDa bands of varying intensity across all the time intervals during the bacterial growth except in the initial hours. Statistically, spontaneously induced HMW putative ABPs of Bl 1951 exhibited a significant decrease in the number of viable cells of its producer strain after 18 h of growth in liquid. In addition, a significant change in pH and prominent bioactivity of the CFS of this particular time period was noted. Biochemically, the filtered supernatant derived from either Bl 1821L or Bl 1951 maintained bioactivity over a wide range of pH and temperature. CONCLUSION This study reports the spontaneous induction of HMW putative ABPs (bacteriocins) of Bl 1821L and Bl 1951 isolates during the course of growth with potential autocidal activity which is critically important during production as a potential biopesticide. A narrow spectrum of putative antibacterial activity of Bl 1951 precipitate was found. The stability of HMW putative ABPs of Bl 1821L and Bl 1951 over a wide range of pH and temperature can be useful in expanding the potential of this useful bacterium beyond the insecticidal value.
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Affiliation(s)
- Tauseef K Babar
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand.
- Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Travis R Glare
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - John G Hampton
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - Mark R H Hurst
- Resilient agriculture, AgResearch, Lincoln Research Centre, Christchurch, New Zealand
| | - Josefina Narciso
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
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Liu Y, Huang Q, Zhuang Z, Yang H, Gou X, Xu T, Liu K, Wang J, Liu B, Gao P, Cao F, Yang B, Zhang C, Chen M, Fan G. Gut virome alterations in patients with chronic obstructive pulmonary disease. Microbiol Spectr 2024; 12:e0428723. [PMID: 38785444 PMCID: PMC11218493 DOI: 10.1128/spectrum.04287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the primary causes of mortality and morbidity worldwide. The gut microbiome, particularly the bacteriome, has been demonstrated to contribute to the progression of COPD. However, the influence of gut virome on the pathogenesis of COPD is rarely studied. Recent advances in viral metagenomics have enabled the rapid discovery of its remarkable role in COPD. In this study, deep metagenomics sequencing of fecal virus-like particles and bacterial 16S rRNA sequencing was performed on 92 subjects from China to characterize alterations of the gut virome in COPD. Lower richness and diversity of the gut virome were observed in the COPD subjects compared with the healthy individuals. Sixty-four viral species, including Clostridium phage, Myoviridae sp., and Synechococcus phage, showed positive relationships with pulmonary ventilation functions and had markedly declined population in COPD subjects. Multiple viral functions, mainly involved in bacterial susceptibility and the interaction between bacteriophages and bacterial hosts, were significantly declined in COPD. In addition, COPD was characterized by weakened viral-bacterial interactions compared with those in the healthy cohort. The gut virome showed diagnostic performance with an area under the curve (AUC) of 88.7%, which indicates the potential diagnostic value of the gut virome for COPD. These results suggest that gut virome may play an important role in the development of COPD. The information can provide a reference for the future investigation of diagnosis, treatment, and in-depth mechanism research of COPD. IMPORTANCE Previous studies showed that the bacteriome plays an important role in the progression of chronic obstructive pulmonary disease (COPD). However, little is known about the involvement of the gut virome in COPD. Our study explored the disease-specific virome signatures of patients with COPD. We found the diversity and compositions altered of the gut virome in COPD subjects compared with healthy individuals, especially those viral species positively correlated with pulmonary ventilation functions. Additionally, the declined bacterial susceptibility, the interaction between bacteriophages and bacterial hosts, and the weakened viral-bacterial interactions in COPD were observed. The findings also suggested the potential diagnostic value of the gut virome for COPD. The results highlight the significance of gut virome in COPD. The novel strategies for gut virome rectifications may help to restore the balance of gut microecology and represent promising therapeutics for COPD.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qingsong Huang
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenhua Zhuang
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Hongjing Yang
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoling Gou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tong Xu
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Ke Liu
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jun Wang
- Department of Respiratory Medicine, Chengdu Fifth People’s Hospital, Chengdu, China
| | - Bo Liu
- Department of Respiratory Medicine, Chengdu Fifth People’s Hospital, Chengdu, China
| | - Peiyang Gao
- Department of Critical Care Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Feng Cao
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Bin Yang
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, China
| | - Chuantao Zhang
- Department of Respiratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mei Chen
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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10
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Thomas MJN, Brockhurst MA, Coyte KZ. What makes a temperate phage an effective bacterial weapon? mSystems 2024; 9:e0103623. [PMID: 38727217 PMCID: PMC11237456 DOI: 10.1128/msystems.01036-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/02/2024] [Indexed: 06/19/2024] Open
Abstract
Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon. We find that effectiveness is controlled by phage life history traits-in particular, the probability of lysis and induction rate-but that the optimal combination of traits varies with the initial frequency of a lysogen within a population. As a consequence, certain phage weapons can be detrimental when their hosts are rare yet beneficial when their hosts are common, while subtle changes in individual life history traits can completely reverse the impact of an individual phage weapon on lysogen fitness. We confirm key predictions of our model experimentally, using temperate phages isolated from the clinically relevant Liverpool epidemic strain of Pseudomonas aeruginosa. Through these experiments, we further demonstrate that nutrient availability can also play a critical role in driving frequency-dependent patterns in phage-mediated competition. Together, these findings highlight the complex and context-dependent nature of temperate phage weapons and the importance of both ecological and evolutionary processes in shaping microbial community dynamics more broadly. IMPORTANCE Temperate bacteriophages-viruses that integrate within bacterial DNA-are incredibly common within bacterial genomes and can act as powerful self-amplifying weapons. Bacterial hosts that carry temperate bacteriophages can thus gain a fitness advantage within a given niche by killing competitors. But what makes an effective phage weapon? Here, we first use a simple mathematical model to explore the factors determining bacteriophage weapon utility. Our models suggest that bacteriophage weapons are nuanced and context-dependent; an individual bacteriophage may be beneficial or costly depending upon tiny changes to how it behaves or the bacterial community it inhabits. We then confirm these mathematical predictions experimentally, using phages isolated from cystic fibrosis patients. But, in doing so, we also find that another factor-nutrient availability-plays a key role in shaping bacteriophage-mediated competition. Together, our results provide new insights into how temperate bacteriophages modulate bacterial communities.
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Affiliation(s)
- M J N Thomas
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - M A Brockhurst
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - K Z Coyte
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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11
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Debatisse K, Lopez P, Poli M, Rousseau P, Campos M, Coddeville M, Cocaign-Bousquet M, Le Bourgeois P. Redefining the bacteriophage mv4 site-specific recombination system and the sequence specificity of its attB and core-attP sites. Mol Microbiol 2024; 121:1200-1216. [PMID: 38705589 DOI: 10.1111/mmi.15275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024]
Abstract
Through their involvement in the integration and excision of a large number of mobile genetic elements, such as phages and integrative and conjugative elements (ICEs), site-specific recombination systems based on heterobivalent tyrosine recombinases play a major role in genome dynamics and evolution. However, despite hundreds of these systems having been identified in genome databases, very few have been described in detail, with none from phages that infect Bacillota (formerly Firmicutes). In this study, we reanalyzed the recombination module of Lactobacillus delbrueckii subsp. bulgaricus phage mv4, previously considered atypical compared with classical systems. Our results reveal that mv4 integrase is a 369 aa protein with all the structural hallmarks of recombinases from the Tn916 family and that it cooperatively interacts with its recombination sites. Using randomized DNA libraries, NGS sequencing, and other molecular approaches, we show that the 21-bp core-attP and attB sites have structural similarities to classical systems only if considering the nucleotide degeneracy, with two 7-bp inverted regions corresponding to mv4Int core-binding sites surrounding a 7-bp strand-exchange region. We also examined the different compositional constraints in the core-binding regions, which define the sequence space of permissible recombination sites.
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Affiliation(s)
- Kevin Debatisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Pierre Lopez
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Maryse Poli
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Philippe Rousseau
- CBI, LMGM, Université de Toulouse, CNRS, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Manuel Campos
- CBI, LMGM, Université de Toulouse, CNRS, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Michèle Coddeville
- CBI, LMGM, Université de Toulouse, CNRS, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
| | | | - Pascal Le Bourgeois
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
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12
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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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13
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Wang Y, Gao Y, Wang X, Lin Y, Xu G, Yang F, Ni K. Insights into the phage community structure and potential function in silage fermentation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120837. [PMID: 38593737 DOI: 10.1016/j.jenvman.2024.120837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
Abstract
The virus that infects bacteria known as phage, plays a crucial role in the biogeochemical cycling of nutrients. However, the community structure and potential functions of phages in silage fermentation remain largely unexplored. In this study, we utilized viral metagenomics (viromics) to investigate the types, lifestyles, functions, and nutrient utilization patterns of phages in silage. Our findings indicated a high prevalence of annotated phages belonging to Caudovirales and Geplafuvirales, as well as unclassified phages in silage. The predominant host types for these phages were Campylobacterales and Enterobacterales. Virulent phages dominated the silage environment due to their broader range of hosts and enhanced survival capabilities. All identified phages present in silage were found to be non-pathogenic. Although temperate and virulent phages carried distinct genes associated with nutrient cycling processes, the shared genes (prsA) involved in carbon metabolism underscore the potential significance of phages in regulating carbon metabolism in silage. Overall, our findings provide a valuable foundation for further exploring the complex interactions between phages and microorganisms in regulating silage fermentation quality.
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Affiliation(s)
- Yuan Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Yu Gao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Xin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Yanli Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Gang Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China.
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
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14
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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15
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Li D, Liang W, Huang Z, Ma W, Liu Q. The spontaneously produced lysogenic prophage phi456 promotes bacterial resistance to adverse environments and enhances the colonization ability of avian pathogenic Escherichia coli strain DE456. Vet Res 2024; 55:37. [PMID: 38532498 DOI: 10.1186/s13567-024-01292-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
In the last decade, prophages that possess the ability of lysogenic transformation have become increasingly significant. Their transfer and subsequent activity in the host have a significant impact on the evolution of bacteria. Here, we investigate the role of prophage phi456 with high spontaneous induction in the bacterial genome of Avian pathogenic Escherichia coli (APEC) DE456. The phage particles, phi456, that were released from DE456 were isolated, purified, and sequenced. Additionally, phage particles were no longer observed either during normal growth or induced by nalidixic acid in DE456Δphi456. This indicated that the released phage particles from DE456 were only phi456. We demonstrated that phi456 contributed to biofilm formation through spontaneous induction of the accompanying increase in the eDNA content. The survival ability of DE456Δphi456 was decreased in avian macrophage HD11 under oxidative stress and acidic conditions. This is likely due to a decrease in the transcription levels of three crucial genes-rpoS, katE, and oxyR-which are needed to help the bacteria adapt to and survive in adverse environments. It has been observed through animal experiments that the presence of phi456 in the DE456 genome enhances colonization ability in vivo. Additionally, the number of type I fimbriae in DE456Δphi456 was observed to be reduced under transmission electron microscopy when compared to the wild-type strain. The qRT-PCR results indicated that the expression levels of the subunit of I fimbriae (fimA) and its apical adhesin (fimH) were significantly lower in DE456Δphi456. Therefore, it can be concluded that phi456 plays a crucial role in helping bacterial hosts survive in unfavorable conditions and enhancing the colonization ability in DE456.
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Affiliation(s)
- Dezhi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Liang
- The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Zhiqiang Huang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenwen Ma
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
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16
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Ji Y, Xi H, Chen C, Sun C, Feng X, Lei L, Han W, Gu J. The pig intestinal phageome is an important reservoir and transfer vector for virulence genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170076. [PMID: 38220020 DOI: 10.1016/j.scitotenv.2024.170076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.
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Affiliation(s)
- Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Changjiang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liancheng Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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17
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Sheng Q, Xu Q, Lan Z, Wu Z. Comparative Genome Analysis of Two Streptococcus suis Serotype 8 Strains Identifies Two New Virulence-Associated Genes. Animals (Basel) 2024; 14:572. [PMID: 38396540 PMCID: PMC10886379 DOI: 10.3390/ani14040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Streptococcus suis is an important zoonotic pathogen that can cause meningitis and septicemia in swine and humans. Among numerous pathogenic serotypes, S. suis serotype 8 has distinctive characteristics such as a high detection rate and causing multi-host infection. There is no complete genome of serotype 8 strains so far. In this study, the complete genome of two S. suis serotype 8 strains, virulent strain 2018WUSS151 and non-virulent strain WUSS030, were sequenced. Comparative genomic analysis showed that the homology of the two genomes reaches 99.68%, and the main difference is the distinctive prophages. There are 83 genes unique to virulent strain 2018WUSS151, including three putative virulence-associated genes (PVGs). Two PVGs, padR and marR, are passenger genes in ISSsu2 family transposons that are able to form circular DNA intermediates during transposition, indicating the possibility of horizontal transmission among S. suis strains. The deletion mutant of PVGs marR or atpase attenuated the virulence of serotype 2 virulent SC070731 in a mouse infection model, confirming their role in S. suis virulence. These findings contribute to clarifying the genomic characterization of S. suis serotype 8 and S. suis pathogenesis.
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Affiliation(s)
- Qi Sheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Qiuhua Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Zouran Lan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Shandong Provincial Center for Animal Disease Control, Jinan 250100, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
- Guangdong Provincial Key Laboratory of Research on the Technology of Pig-Breeding and Pig-Disease Prevention, Guangzhou 511400, China
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18
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Gong C, Chakraborty D, Koudelka GB. A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC). Nucleic Acids Res 2024; 52:856-871. [PMID: 38084890 PMCID: PMC10810198 DOI: 10.1093/nar/gkad1150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 01/26/2024] Open
Abstract
Shiga toxin (Stx) released by Shiga toxin producing Escherichia coli (STEC) causes life-threatening illness. Its production and release require induction of Stx-encoding prophage resident within the STEC genome. We identified two different STEC strains, PA2 and PA8, bearing Stx-encoding prophage whose sequences primarily differ by the position of an IS629 insertion element, yet differ in their abilities to kill eukaryotic cells and whose prophages differ in their spontaneous induction frequencies. The IS629 element in ϕPA2, disrupts an ORF predicted to encode a DNA adenine methyltransferase, whereas in ϕPA8, this element lies in an intergenic region. Introducing a plasmid expressing the methyltransferase gene product into ϕPA2 bearing-strains increases both the prophage spontaneous induction frequency and virulence to those exhibited by ϕPA8 bearing-strains. However, a plasmid bearing mutations predicted to disrupt the putative active site of the methyltransferase does not complement either of these defects. When complexed with a second protein, the methyltransferase holoenzyme preferentially uses 16S rRNA as a substrate. The second subunit is responsible for directing the preferential methylation of rRNA. Together these findings reveal a previously unrecognized role for rRNA methylation in regulating induction of Stx-encoding prophage.
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Affiliation(s)
- Chen Gong
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
| | | | - Gerald B Koudelka
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
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19
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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20
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Lou YC, Chen L, Borges AL, West-Roberts J, Firek BA, Morowitz MJ, Banfield JF. Infant gut DNA bacteriophage strain persistence during the first 3 years of life. Cell Host Microbe 2024; 32:35-47.e6. [PMID: 38096814 PMCID: PMC11156429 DOI: 10.1016/j.chom.2023.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
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21
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Liu Z, Tang K, Zhou Y, Liu T, Guo Y, Wu D, Wang X. Active prophages in coral-associated Halomonas capable of lateral transduction. THE ISME JOURNAL 2024; 18:wrae085. [PMID: 38739683 PMCID: PMC11131426 DOI: 10.1093/ismejo/wrae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.
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Affiliation(s)
- Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yiqing Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Duoting Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
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22
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Vale FF, Roberts RJ, Kobayashi I, Camargo MC, Rabkin CS. Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project. Gut Microbes 2024; 16:2379440. [PMID: 39132840 PMCID: PMC11321410 DOI: 10.1080/19490976.2024.2379440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/19/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.
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Affiliation(s)
- Filipa F Vale
- BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | | | - Ichizo Kobayashi
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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23
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Weinroth MD, Clawson ML, Harhay GP, Eppinger M, Harhay DM, Smith TPL, Bono JL. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Front Microbiol 2023; 14:1303387. [PMID: 38169669 PMCID: PMC10758439 DOI: 10.3389/fmicb.2023.1303387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.
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Affiliation(s)
- Margaret D. Weinroth
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Michael L. Clawson
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Dayna M. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Timothy P. L. Smith
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - James L. Bono
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
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24
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Douillard FP, Portinha IM, Derman Y, Woudstra C, Mäklin T, Dorner MB, Korkeala H, Henriques AO, Lindström M. A Novel Prophage-like Insertion Element within yabG Triggers Early Entry into Sporulation in Clostridium botulinum. Viruses 2023; 15:2431. [PMID: 38140671 PMCID: PMC10747680 DOI: 10.3390/v15122431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Sporulation is a finely regulated morphogenetic program important in the ecology and epidemiology of Clostridium botulinum. Exogenous elements disrupting sporulation-associated genes contribute to sporulation regulation and introduce diversity in the generally conserved sporulation programs of endospore formers. We identified a novel prophage-like DNA segment, termed the yin element, inserted within yabG, encoding a sporulation-specific cysteine protease, in an environmental isolate of C. botulinum. Bioinformatic analysis revealed that the genetic structure of the yin element resembles previously reported mobile intervening elements associated with sporulation genes. Within a pure C. botulinum culture, we observed two subpopulations of cells with the yin element either integrated into the yabG locus or excised as a circular DNA molecule. The dynamics between the two observed conformations of the yin element was growth-phase dependent and likely mediated by recombination events. The yin element was not required for sporulation by C. botulinum but triggered an earlier entry into sporulation than in a related isolate lacking this element. So far, the yin element has not been found in any other C. botulinum strains or other endospore-forming species. It remains to be demonstrated what kind of competitive edge it provides for C. botulinum survival and persistence.
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Affiliation(s)
- François P. Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00350 Helsinki, Finland; (F.P.D.); (I.M.P.); (Y.D.); (C.W.); (H.K.)
| | - Inês Martins Portinha
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00350 Helsinki, Finland; (F.P.D.); (I.M.P.); (Y.D.); (C.W.); (H.K.)
| | - Yağmur Derman
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00350 Helsinki, Finland; (F.P.D.); (I.M.P.); (Y.D.); (C.W.); (H.K.)
| | - Cédric Woudstra
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00350 Helsinki, Finland; (F.P.D.); (I.M.P.); (Y.D.); (C.W.); (H.K.)
| | - Tommi Mäklin
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, 00560 Helsinki, Finland;
| | - Martin B. Dorner
- Centre for Biological Threats and Special Pathogens, ZBS3—Biological Toxins, Robert Koch Institute, 13353 Berlin, Germany;
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00350 Helsinki, Finland; (F.P.D.); (I.M.P.); (Y.D.); (C.W.); (H.K.)
| | - Adriano O. Henriques
- Institute of Chemical and Biological Technology, NOVA University Lisbon, 2780-157 Oeiras, Portugal;
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00350 Helsinki, Finland; (F.P.D.); (I.M.P.); (Y.D.); (C.W.); (H.K.)
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25
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Li L, Hu Z, Tan G, Fan J, Chen Y, Xiao Y, Wu S, Zhi Q, Liu T, Yin H, Tang Q. Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities. FRONTIERS IN PLANT SCIENCE 2023; 14:1259853. [PMID: 38034579 PMCID: PMC10683058 DOI: 10.3389/fpls.2023.1259853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.
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Affiliation(s)
- Liangzhi Li
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhengrong Hu
- Hunan Tobacco Research Institute, Changsha, China
| | - Ge Tan
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian, China
| | - Yiqiang Chen
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, China
| | - Qiqi Zhi
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Tianbo Liu
- Hunan Tobacco Research Institute, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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26
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An T, Cai Y, Li G, Li S, Wong PK, Guo J, Zhao H. Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture. ISME COMMUNICATIONS 2023; 3:115. [PMID: 37935916 PMCID: PMC10630474 DOI: 10.1038/s43705-023-00321-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
Due to the wide use of antibiotics, intensive aquaculture farms have been recognized as a significant reservoir of antibiotic resistomes. Although the prevalence of colistin resistance genes and multidrug-resistant bacteria (MDRB) has been documented, empirical evidence for the transmission of colistin and multidrug resistance between bacterial communities in aquaculture farms through horizontal gene transfer (HGT) is lacking. Here, we report the prevalence and transmission risk of colistin and multidrug resistance in 27 aquaculture water samples from 9 aquaculture zones from over 5000 km of subtropical coastlines in southern China. The colistin resistance gene mcr-1, mobile genetic element (MGE) intl1 and 13 typical antibiotic resistance genes (ARGs) were prevalent in all the aquaculture water samples. Most types of antibiotic (especially colistin) resistance are transmissible in bacterial communities based on evidence from laboratory conjugation and transformation experiments. Diverse MDRB were detected in most of the aquaculture water samples, and a strain with high-level colistin resistance, named Ralstonia pickettii MCR, was isolated. The risk of horizontal transfer of the colistin resistance of R. pickettii MCR through conjugation and transformation was low, but the colistin resistance could be steadily transmitted to offspring through vertical transfer. The findings have important implications for the future regulation of antibiotic use in aquaculture farms globally to address the growing threat posed by antibiotic resistance to human health.
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Affiliation(s)
- Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China.
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Yiwei Cai
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Guiying Li
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Shaoting Li
- College of Biological and Pharmaceutical Science, Guangdong University of Technology, Guangzhou, 510006, China
| | - Po Keung Wong
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.
| | - Huijun Zhao
- Centre for Clean Environment and Energy, and Griffith School of Environment, Gold Coast Campus, Griffith University, Gold Coast, QLD, 4222, Australia
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27
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Sudhakari PA, Ramisetty BCM. An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages. MICROBIAL ECOLOGY 2023; 86:3068-3081. [PMID: 37843655 DOI: 10.1007/s00248-023-02301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, 312@ASK1, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, 312@ASK1, Thanjavur, India.
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28
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Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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29
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Young GR, Nelson A, Stewart CJ, Smith DL. Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease. Curr Opin Microbiol 2023; 75:102379. [PMID: 37647765 DOI: 10.1016/j.mib.2023.102379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Abstract
Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.
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Affiliation(s)
- Gregory R Young
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Andrew Nelson
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | | | - Darren L Smith
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK.
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30
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Yi Y, Liu S, Hao Y, Sun Q, Lei X, Wang Y, Wang J, Zhang M, Tang S, Tang Q, Zhang Y, Liu X, Wang Y, Xiao X, Jian H. A systematic analysis of marine lysogens and proviruses. Nat Commun 2023; 14:6013. [PMID: 37758717 PMCID: PMC10533544 DOI: 10.1038/s41467-023-41699-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
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Affiliation(s)
- Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinjuan Lei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yecheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingxue Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xipeng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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Huang J, Dai X, Wu Z, Hu X, Sun J, Tang Y, Zhang W, Han P, Zhao J, Liu G, Wang X, Mao S, Wang Y, Call DR, Liu J, Wang L. Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes. THE ISME JOURNAL 2023; 17:1467-1481. [PMID: 37369704 PMCID: PMC10432423 DOI: 10.1038/s41396-023-01463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.
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Affiliation(s)
- Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqiu Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangjin Liu
- Key Lab of Animal Bacteriology, Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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32
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Xiong L, Li Y, Yu H, Wei Y, Li H, Ji X. Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland. Sci Rep 2023; 13:14190. [PMID: 37648730 PMCID: PMC10468529 DOI: 10.1038/s41598-023-41323-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
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33
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Frazão N, Gordo I. Ecotype formation and prophage domestication during gut bacterial evolution. Bioessays 2023; 45:e2300063. [PMID: 37353919 DOI: 10.1002/bies.202300063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/25/2023]
Abstract
How much bacterial evolution occurs in our intestines and which factors control it are currently burning questions. The formation of new ecotypes, some of which capable of coexisting for long periods of time, is highly likely in our guts. Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals. Also see the video abstract here: https://youtu.be/Zjqsiyb5Pk0.
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Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Zhang M, Hao Y, Yi Y, Liu S, Sun Q, Tan X, Tang S, Xiao X, Jian H. Unexplored diversity and ecological functions of transposable phages. THE ISME JOURNAL 2023; 17:1015-1028. [PMID: 37069234 PMCID: PMC10284936 DOI: 10.1038/s41396-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.
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Affiliation(s)
- Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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35
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Chacón L, Kuropka B, González-Tortuero E, Schreiber F, Rojas-Jiménez K, Rodríguez-Rojas A. Mechanisms of low susceptibility to the disinfectant benzalkonium chloride in a multidrug-resistant environmental isolate of Aeromonas hydrophila. Front Microbiol 2023; 14:1180128. [PMID: 37333642 PMCID: PMC10272739 DOI: 10.3389/fmicb.2023.1180128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/04/2023] [Indexed: 06/20/2023] Open
Abstract
Excessive discharge of quaternary ammonium disinfectants such as benzalkonium chloride (BAC) into aquatic systems can trigger several physiological responses in environmental microorganisms. In this study, we isolated a less-susceptible strain of Aeromonas hydrophila to BAC, designated as INISA09, from a wastewater treatment plant in Costa Rica. We characterized its phenotypic response upon exposure to three different concentrations of BAC and characterized mechanisms related to its resistance using genomic and proteomic approaches. The genome of the strain, mapped against 52 different sequenced A. hydrophila strains, consists of approximately 4.6 Mb with 4,273 genes. We found a massive genome rearrangement and thousands of missense mutations compared to the reference strain A. hydrophila ATCC 7966. We identified 15,762 missense mutations mainly associated with transport, antimicrobial resistance, and outer membrane proteins. In addition, a quantitative proteomic analysis revealed a significant upregulation of several efflux pumps and the downregulation of porins when the strain was exposed to three BAC concentrations. Other genes related to membrane fatty acid metabolism and redox metabolic reactions also showed an altered expression. Our findings indicate that the response of A. hydrophila INISA09 to BAC primarily occurs at the envelop level, which is the primary target of BAC. Our study elucidates the mechanisms of antimicrobial susceptibility in aquatic environments against a widely used disinfectant and will help better understand how bacteria can adapt to biocide pollution. To our knowledge, this is the first study addressing the resistance to BAC in an environmental A. hydrophila isolate. We propose that this bacterial species could also serve as a new model to study antimicrobial pollution in aquatic environments.
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Affiliation(s)
- Luz Chacón
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Health Research Institute, University of Costa Rica, San José, Costa Rica
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Enrique González-Tortuero
- School of Science, Engineering, and Environment (SEE), University of Salford, Manchester, United Kingdom
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | | | - Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Small Animal Internal Medicine, Clinic for Small Animals, University of Veterinary Medicine (Vetmeduni), Vienna, Austria
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36
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Deng X, Yuan J, Chen L, Chen H, Wei C, Nielsen PH, Wuertz S, Qiu G. CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. WATER RESEARCH 2023; 235:119906. [PMID: 37004306 DOI: 10.1016/j.watres.2023.119906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.
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Affiliation(s)
- Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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37
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Huang D, Yuan MM, Chen J, Zheng X, Wong D, Alvarez PJJ, Yu P. The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes. ISME COMMUNICATIONS 2023; 3:46. [PMID: 37142716 PMCID: PMC10160068 DOI: 10.1038/s43705-023-00249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of prokaryotic community. However, the prokaryotic antiviral systems under environmental stress are poorly understood, limiting the understanding of microbial adaptability. Here, we systematically investigated the profile of the prokaryotic antiviral systems at the community level and prokaryote-phage interactions in the drinking water microbiome. Chlorine disinfectant was revealed as the main ecological driver for the difference in prokaryotic antiviral systems and prokaryote-phage interactions. Specifically, the prokaryotic antiviral systems in the microbiome exhibited a higher abundance, broader antiviral spectrum, and lower metabolic burden under disinfectant stress. Moreover, significant positive correlations were observed between phage lysogenicity and enrichment of antiviral systems (e.g., Type IIG and IV restriction-modification (RM) systems, and Type II CRISPR-Cas system) in the presence of disinfection, indicating these antiviral systems might be more compatible with lysogenic phages and prophages. Accordingly, there was a stronger prokaryote-phage symbiosis in disinfected microbiome, and the symbiotic phages carried more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability as well as antiviral systems, which might further enhance prokaryote survival in drinking water distribution systems. Overall, this study demonstrates that the prokaryotic antiviral systems had a close association with their symbiotic phages, which provides novel insights into prokaryote-phage interactions and microbial environmental adaptation.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoxuan Zheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Dongsheng Wong
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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Gaougaou G, Vincent AT, Krylova K, Habouria H, Bessaiah H, Baraketi A, Veyrier FJ, Dozois CM, Déziel E, Lacroix M. Adaptive Radioresistance of Enterohemorrhagic Escherichia coli O157:H7 Results in Genomic Loss of Shiga Toxin-Encoding Prophages. Appl Environ Microbiol 2023; 89:e0130622. [PMID: 37014232 PMCID: PMC10132102 DOI: 10.1128/aem.01306-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/10/2023] [Indexed: 04/05/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen producing Shiga toxins (Stx1 and Stx2), which can cause hemorrhagic diarrhea and life-threatening infections. O157:H7 strain EDL933 carries prophages CP-933V and BP-933W, which encode Shiga toxin genes (stx1 and stx2, respectively). The aim of this work was to investigate the mechanisms of adaptive resistance of EHEC strain EDL933 to a typically lethal dose of gamma irradiation (1.5 kGy). Adaptive selection through six passages of exposure to 1.5 kGy resulted in the loss of CP-933V and BP-933W prophages from the genome and mutations within three genes: wrbA, rpoA, and Wt_02639 (molY). Three selected EHEC clones that became irradiation adapted to the 1.5-kGy dose (C1, C2, and C3) demonstrated increased resistance to oxidative stress, sensitivity to acid pH, and decreased cytotoxicity to Vero cells. To confirm that loss of prophages plays a role in increased radioresistance, clones C1 and C2 were exposed to bacteriophage-containing lysates. Although phage BP-933W could lysogenize C1, C2, and E. coli K-12 strain MG1655, it was not found to have integrated into the bacterial chromosome in C1-Φ and C2-Φ lysogens. Interestingly, for the E. coli K-12 lysogen (K-12-Φ), BP-933W DNA had integrated at the wrbA gene (K-12-Φ). Both C1-Φ and C2-Φ lysogens regained sensitivity to oxidative stress, were more effectively killed by a 1.5-kGy gamma irradiation dose, and had regained cytotoxicity and acid resistance phenotypes. Further, the K-12-Φ lysogen became cytotoxic, more sensitive to gamma irradiation and oxidative stress, and slightly more acid resistant. IMPORTANCE Gamma irradiation of food products can provide an effective means of eliminating bacterial pathogens such as enterohemorrhagic Escherichia coli (EHEC) O157:H7, a significant foodborne pathogen that can cause severe disease due to the production of Stx. To decipher the mechanisms of adaptive resistance of the O157:H7 strain EDL933, we evolved clones of this bacterium resistant to a lethal dose of gamma irradiation by repeatedly exposing bacterial cells to irradiation following a growth restoration over six successive passages. Our findings provide evidence that adaptive selection involved modifications in the bacterial genome, including deletion of the CP-933V and BP-933W prophages. These mutations in EHEC O157:H7 resulted in loss of stx1 and stx2, loss of cytotoxicity to epithelial cells, and decreased resistance to acidity, critical virulence determinants of EHEC, concomitant with increased resistance to lethal irradiation and oxidative stress. These findings demonstrate that the potential adaptation of EHEC to high doses of radiation would involve elimination of the Stx-encoding phages and likely lead to a substantial attenuation of virulence.
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Affiliation(s)
- Ghizlane Gaougaou
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Research Laboratories in Sciences Applied to Food, Canadian Irradiation Centre, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Antony T. Vincent
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Kateryna Krylova
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Hajer Habouria
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Hicham Bessaiah
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Amina Baraketi
- Research Laboratories in Sciences Applied to Food, Canadian Irradiation Centre, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | | | - Charles M. Dozois
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Eric Déziel
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | - Monique Lacroix
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Research Laboratories in Sciences Applied to Food, Canadian Irradiation Centre, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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Wang S, Mirmiran SD, Li X, Li X, Zhang F, Duan X, Gao D, Chen Y, Chen H, Qian P. Temperate phage influence virulence and biofilm-forming of Salmonella Typhimurium and enhance the ability to contaminate food product. Int J Food Microbiol 2023; 398:110223. [PMID: 37120944 DOI: 10.1016/j.ijfoodmicro.2023.110223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Salmonella is a food-borne zoonotic pathogen that threatens food safety and public health security. Temperate phages can influence bacterial virulence and phenotype and play an important role in bacterial evolution. However, most studies on Salmonella temperate phages focus on prophage induced by bacteria, with few reports on Salmonella temperate phages isolated in the environment. Moreover, whether temperate phages drive bacterial virulence and biofilm formation in food and animal models remains unknown. In this study, Salmonella temperate phage vB_Sal_PHB48 was isolated from sewage. TEM and phylogenetic analysis indicated that phage PHB48 belongs to the Myoviridae family. Additionally, Salmonella Typhimurium integrating PHB48 was screened and designated as Sal013+. Whole genome sequencing revealed that the integration site was specific and we confirmed that the integration of PHB48 did not change the O-antigen and coding sequences of Sal013. Our in vitro and in vivo studies showed that the integration of PHB48 could significantly enhance the virulence and biofilm formation of S. Typhimurium. More importantly, the integration of PHB48 significantly improved the colonization and contamination ability of bacteria in food samples. In conclusion, we isolated Salmonella temperate phage directly from the environment and systematically clarified that PHB48 enhanced the virulence and biofilm-forming ability of Salmonella. In addition, we found that PHB48 increased the colonization and contamination ability of Salmonella in food samples. These results indicated that the highly pathogenic Salmonella induced by temperate phage was more harmful to food matrices and public health security. Our results could enhance the understanding of the evolutionary relationship between bacteriophages and bacteria, and raise public awareness of large-scale outbreaks resulting from Salmonella virulence enhancement in food industry.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Seyyed Danial Mirmiran
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xiangmin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xinxin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Fenqiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xiaochao Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Dongyang Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yibao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China.
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40
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Xia R, Sun M, Balcázar JL, Yu P, Hu F, Alvarez PJJ. Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes. THE ISME JOURNAL 2023:10.1038/s41396-023-01408-x. [PMID: 37069233 DOI: 10.1038/s41396-023-01408-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg-1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg-1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.
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Affiliation(s)
- Rong Xia
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China
| | - Mingming Sun
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China.
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003, Girona, Spain
- University of Girona, 17004, Girona, Spain
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310085, China.
| | - Feng Hu
- Soil Ecology Lab, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China
| | - Pedro J J Alvarez
- Civil and Environmental Engineering Department, Rice University, Houston, TX, 77005, USA
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41
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Cuellar-Gaviria TZ, García-Botero C, Ju KS, Villegas-Escobar V. The genome of Bacillus tequilensis EA-CB0015 sheds light into its epiphytic lifestyle and potential as a biocontrol agent. Front Microbiol 2023; 14:1135487. [PMID: 37051516 PMCID: PMC10083409 DOI: 10.3389/fmicb.2023.1135487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Different Bacillus species have successfully been used as biopesticides against a broad range of plant pathogens. Among these, Bacillus tequilensis EA-CB0015 has shown to efficiently control Black sigatoka disease in banana plants, presumably by mechanisms of adaptation that involve modifying the phyllosphere environment. Here, we report the complete genome of strain EA-CB0015, its precise taxonomic identity, and determined key genetic features that may contribute to its effective biocontrol of plant pathogens. We found that B. tequilensis EA-CB0015 harbors a singular 4 Mb circular chromosome, with 3,951 protein-coding sequences. Multi-locus sequence analysis (MLSA) and average nucleotide identity (ANI) analysis classified strain EA-CB0015 as B. tequilensis. Encoded within its genome are biosynthetic gene clusters (BGCs) for surfactin, iturin, plipastatin, bacillibactin, bacilysin, subtilosin A, sporulation killing factor, and other natural products that may facilitate inter-microbial warfare. Genes for indole-acetic acid (IAA) synthesis, the use of diverse carbon sources, and a multicellular lifestyle involving motility, biofilm formation, quorum sensing, competence, and sporulation suggest EA-CB0015 is adept at colonizing plant surfaces. Defensive mechanisms to survive invading viral infections and preserve genome integrity include putative type I and type II restriction modification (RM) and toxin/antitoxin (TA) systems. The presence of bacteriophage sequences, genomic islands, transposable elements, virulence factors, and antibiotic resistance genes indicate prior occurrences of genetic exchange. Altogether, the genome of EA-CB0015 supports its function as a biocontrol agent against phytopathogens and suggest it has adapted to thrive within phyllosphere environments.
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Affiliation(s)
- Tatiana Z. Cuellar-Gaviria
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Banana Research Center, Augura, Conjunto Residencial Los Almendros, Carepa, Colombia
| | - Camilo García-Botero
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, OH, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Kou-San Ju, ; Valeska Villegas-Escobar,
| | - Valeska Villegas-Escobar
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
- *Correspondence: Kou-San Ju, ; Valeska Villegas-Escobar,
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42
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Sharma V, Hünnefeld M, Luthe T, Frunzke J. Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity. Sci Rep 2023; 13:4410. [PMID: 36932119 PMCID: PMC10023795 DOI: 10.1038/s41598-023-30829-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum.
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Affiliation(s)
- Vikas Sharma
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Max Hünnefeld
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Tom Luthe
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
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43
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Tu Q, Pu M, Li Y, Wang Y, Li M, Song L, Li M, An X, Fan H, Tong Y. Acinetobacter Baumannii Phages: Past, Present and Future. Viruses 2023; 15:v15030673. [PMID: 36992382 PMCID: PMC10057898 DOI: 10.3390/v15030673] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common clinical pathogens and a typical multi-drug resistant (MDR) bacterium. With the increase of drug-resistant A. baumannii infections, it is urgent to find some new treatment strategies, such as phage therapy. In this paper, we described the different drug resistances of A. baumannii and some basic properties of A. baumannii phages, analyzed the interaction between phages and their hosts, and focused on A. baumannii phage therapies. Finally, we discussed the chance and challenge of phage therapy. This paper aims to provide a more comprehensive understanding of A. baumannii phages and theoretical support for the clinical application of A. baumannii phages.
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Affiliation(s)
- Qihang Tu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mingfang Pu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yahao Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
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44
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Mayers KMJ, Kuhlisch C, Basso JTR, Saltvedt MR, Buchan A, Sandaa RA. Grazing on Marine Viruses and Its Biogeochemical Implications. mBio 2023; 14:e0192121. [PMID: 36715508 PMCID: PMC9973340 DOI: 10.1128/mbio.01921-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.
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Affiliation(s)
- Kyle M. J. Mayers
- Environment and Climate Division, NORCE Norwegian Research Centre, Bergen, Norway
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jonelle T. R. Basso
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | | | - Alison Buchan
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - Ruth-Anne Sandaa
- Department of Microbiology, University of Bergen, Bergen, Norway
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45
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Stockdale SR, Shkoporov AN, Khokhlova EV, Daly KM, McDonnell SA, O' Regan O, Nolan JA, Sutton TDS, Clooney AG, Ryan FJ, Sheehan D, Lavelle A, Draper LA, Shanahan F, Ross RP, Hill C. Interpersonal variability of the human gut virome confounds disease signal detection in IBD. Commun Biol 2023; 6:221. [PMID: 36841913 PMCID: PMC9968284 DOI: 10.1038/s42003-023-04592-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/14/2023] [Indexed: 02/27/2023] Open
Abstract
Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohn's disease, and 20 ulcerative colitis viromes over three time points without an amplification bias, which revealed and highlighted the interpersonal individuality of the human gut virome. In contrast to a 16 S rRNA gene analysis of matched samples, we show that α- and β-diversity metrics of unamplified viromes are not as efficient at discerning controls from patients with inflammatory bowel disease. Additionally, we explored the intrinsic properties of unamplified gut viromes and show there is considerable interpersonal variability in viral taxa, infrequent longitudinal persistence of intrapersonal viruses, and vast fluctuations in the abundance of temporal viruses. Together, these properties of unamplified faecal viromes confound the ability to discern disease associations but significantly advance toward an unbiased and accurate representation of the human gut virome.
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Affiliation(s)
| | | | | | - Karen M Daly
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | | | - Orla O' Regan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - James A Nolan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | | | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Feargal J Ryan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Donal Sheehan
- Department of Medicine, University College Cork, Co, Cork, Ireland
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
- Department of Medicine, University College Cork, Co, Cork, Ireland
| | | | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
- Department of Medicine, University College Cork, Co, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland.
- School of Microbiology, University College Cork, Co, Cork, Ireland.
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46
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Unveil the Secret of the Bacteria and Phage Arms Race. Int J Mol Sci 2023; 24:ijms24054363. [PMID: 36901793 PMCID: PMC10002423 DOI: 10.3390/ijms24054363] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage's nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and other defense systems to interfere with the replication of phage genes in the host; through the quorum sensing (QS) enhancement of phage's resistant effect. At the same time, phages have also evolved a variety of counter-defense strategies, such as degrading extracellular polymeric substances (EPS) that mask receptors or recognize new receptors, thereby regaining the ability to adsorb host cells; modifying its own genes to prevent the R-M systems from recognizing phage genes or evolving proteins that can inhibit the R-M complex; through the gene mutation itself, building nucleus-like compartments or evolving anti-CRISPR (Acr) proteins to resist CRISPR-Cas systems; and by producing antirepressors or blocking the combination of autoinducers (AIs) and its receptors to suppress the QS. The arms race between bacteria and phages is conducive to the coevolution between bacteria and phages. This review details bacterial anti-phage strategies and anti-defense strategies of phages and will provide basic theoretical support for phage therapy while deeply understanding the interaction mechanism between bacteria and phages.
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47
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Ma R, Chen X, Li Y, Jiao N, Zhang R. Diversity, evolution and life strategies of CbK-like phages. Environ Microbiol 2023. [PMID: 36807729 DOI: 10.1111/1462-2920.16354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Caulobacter phage CbK has been extensively studied as a model system in virology and bacteriology. Lysogeny-related genes have been found in each CbK-like isolate, suggesting a life strategy of both lytic and lysogenic cycles. However, whether CbK-related phages can enter lysogeny is still undetermined. This study identified new CbK-like sequences and expanded the collection of CbK-related phages. A common ancestry with a temperate lifestyle was predicted for the group, however, which subsequently evolved into two clades of different genome sizes and host associations. Through the examination of phage recombinase genes, alignment of attachment sites on the phage and bacterial genomes (attP-attB pairing), and the experimental validation, different lifestyles were found among the different members. A majority of clade II members retain a lysogenic lifestyle, whereas all clade I members have evolved into an obligate lytic lifestyle via a loss of the gene encoding Cre-like recombinase and the coupled attP fragment. We postulated that the loss of lysogeny may be a by-product of the increase in phage genome size, and vice versa. Clade I is likely to overcome the costs through maintaining more auxiliary metabolic genes (AMGs), particularly for those involved in protein metabolism, to strengthen host takeover and further benefit virion production.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yingying Li
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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48
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Gummalla VS, Zhang Y, Liao YT, Wu VCH. The Role of Temperate Phages in Bacterial Pathogenicity. Microorganisms 2023; 11:541. [PMID: 36985115 PMCID: PMC10052878 DOI: 10.3390/microorganisms11030541] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/05/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage-bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments.
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Affiliation(s)
| | | | | | - Vivian C. H. Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA
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Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses. mBio 2023; 14:e0249022. [PMID: 36779718 PMCID: PMC10127798 DOI: 10.1128/mbio.02490-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.
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Ji Y, Xi H, Zhao Z, Jiang Q, Chen C, Wang X, Li F, Li N, Sun C, Feng X, Lei L, Han W, Gu J. Metagenomics analysis reveals potential pathways and drivers of piglet gut phage-mediated transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160304. [PMID: 36427721 DOI: 10.1016/j.scitotenv.2022.160304] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
The growing prevalence of antibiotic-resistant pathogens has led to a better understanding of the underlying processes that lead to this expansion. Intensive pig farms are considered one of the hotspots for antibiotic resistance gene (ARG) transmission. Phages, as important mobile carriers of ARGs, are widespread in the animal intestine. However, our understanding of phage-associated ARGs in the pig intestine and their underlying drivers is limited. Here, metagenomic sequencing and analysis of viral DNA and total DNA of different intestinal (ileum, cecum and feces) contents in healthy piglets and piglets with diarrhea were separately conducted. We found that phages in piglet ceca are the main repository for ARGs and mobile genetic element (MGE) genes. Phage-associated MGEs are important factors affecting the maintenance and transfer of ARGs. Interestingly, the colocalization of ARGs and MGE genes in piglet gut phages does not appear to be randomly selected but rather related to a specific phage host (Streptococcus). In addition, in the feces of piglets with diarrhea, the abundance of phages carrying ARGs and MGE genes was significantly increased, as was the diversity of polyvalent phages (phages with broad host ranges), which would facilitate the transfection and wider distribution of ARGs in the bacterial community. Moreover, the predicted host spectrum of polyvalent phages in diarrheal feces tended to be potential enteropathogenic genera, which greatly increased the risk of enteropathogens acquiring ARGs. Notably, we also found ARG-homologous genes in the sequences of piglet intestinal mimiviruses, suggesting that the piglet intestinal mimiviruses are a potential repository of ARGs. In conclusion, this study greatly expands our knowledge of the piglet gut microbiome, revealing the underlying mechanisms of maintenance and dissemination of piglet gut ARGs and providing a reference for the prevention and control of ARG pollution in animal husbandry.
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Affiliation(s)
- Yalu Ji
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Hengyu Xi
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Zhen Zhao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Qiujie Jiang
- Jilin Animal Disease Control Center, Changchun 130062, People's Republic of China
| | - Chong Chen
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Xinwu Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Fengyang Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Na Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Changjiang Sun
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Xin Feng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Liancheng Lei
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China
| | - Wenyu Han
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, People's Republic of China.
| | - Jingmin Gu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, People's Republic of China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, People's Republic of China.
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